Finally, I thought I summarise the documentation of MAUI Schduler Commands in one nice blog entry "Overview of MAUI Scheduler Commands". Hopefully, this will help summarise the commands used for system administration of the MAUI Scheduler

The Phoronix Test Suite is the most comprehensive testing and benchmarking platform available for the Linux operating system. This software is designed to effectively carry out both qualitative and quantitative benchmarks in a clean, reproducible, and easy-to-use manner. The Phoronix Test Suite consists of a lightweight processing core (pts-core) with each benchmark consisting of an XML-based profile with related resource scripts. Some of the key features are

Sunday, February 21, 2010

Inkscape is an Open Source vector graphics editor, with capabilities similar to Illustrator, CorelDraw, or Xara X, using the W3C standard Scalable Vector Graphics (SVG) file format.

Inkscape supports many advanced SVG features (markers, clones, alpha blending, etc.) and great care is taken in designing a streamlined interface. It is very easy to edit nodes, perform complex path operations, trace bitmaps and much more. We also aim to maintain a thriving user and developer community by using open, community-oriented development.'

Saturday, February 20, 2010

There are many ways to send a large file across. Using Bittorrent, P2P, FTP etc. But what if you encounter scenario like sending a email attachment with very limited attachment size, you may find this tool useful

For example, you have a media file of size 20M and you wish to break it up to 10M chunk, just use the split command that comes with Linux

split -b 10M test-split.wmv

Consequently, the command will break the test-split.wmv into 2 chunk xaa and xab. "xaa" and "xab" are generated by the split command. If you split into more chunk, it will follow the alphabetical order xac, xad etc

To join back the 2 file into a single entity again, just use the good old cat

Friday, February 19, 2010

Actually from htop and top utilities, you can find how the memory is used and buffered.

When you run top, you will notice that a lot of memory are being used even though there may not be much applications currently running. The reasons for this huge usage is that the kernel allocates memory that isn't in active use by processes to things like filesystem caches to improve performance. If there is demand on the memory by another application or data, the kernel will free up the memory.

If you run top, you will notice buffers and cached. "Buffers" represent how much portion of RAM is dedicated to cache disk block. "Cached" is similar like "Buffers", only this time it caches pages from file reading.

However if you run htop, the memory used is smaller. Both utilities are not wrong, it is a different representation of the memory usage

Friday, February 12, 2010

OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.

Thursday, February 11, 2010

ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.4 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux.

It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.

It can calculate area and pixel value statistics of user-defined selections. It can measure distances and angles. It can create density histograms and line profile plots. It supports standard image processing functions such as contrast manipulation, sharpening, smoothing, edge detection and median filtering.

Wednesday, February 10, 2010

NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PL0OR.

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.

Monday, February 8, 2010

DeVeDe is a program to create video DVDs and CDs (VCD, sVCD or CVD), suitables for home players, from any number of video files, in any of the formats supported by Mplayer. The big advantage over other utilites is that it only needs Mplayer, Mencoder, DVDAuthor, VCDImager and MKisofs (well, and Python, PyGTK and PyGlade), so its dependencies are really small.

To install devede on Fedora 11, first you have to install RPM Fusion. For more information on RPM Fusion installation, see Blog Entry RPM Fusion Repository. Remember to do a "yum check-update" after you have install the repository

Wednesday, February 3, 2010

One obvious symptoms of this problem is that it was possible to SSH in from external machine, but was unable SSH out of the problematic machine

To resolve this issue, you have to go to

$ cd /home/youruserid/.ssh/
$ vim config

Change the configuration to

BatchMode no

The option BatchMode specifies whether a username and password querying on connect will be disabled. This option is useful when you create scripts and dont want to supply the password. e.g. Scripts that use the scp command to make backups over the network.

This resolution to the issue can be found at OpenMPI FAQ to resolve this issue, you have to include the

$ mpicc hello.c -o hello -shared-intel

The default behavior of Open MPI's wrapper compilers can be changed to automatically include this -shared-intel flag so that it is unnecessary to specify it on the command line when linking MPI applications.

The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.

PUPIL,Program for User Package Interface and Linking, is a software environment,- the program,- to allow developers to quickly and efficiently link together multiple pieces of software,- the user packages,- that have been and are actively being developed by researchers.

With its current 1.3 version, it is able to

Graphic User Interface to build the main simulation input file.

Simulation Manager to lead the multi-scale simulation between different Calculation Units.

Interface with Amber v10

Interface with DLPOLY v2.18

Interface with Gaussian03

Interface with deMon2k

Interface with NWChem

Interface with Siesta v2.0 (Start/Stop and CycleQM behaviors)

Interface with mndo97 (Start/Stop QM role behaviors)

stubMD. Stub program for interface sample and testing playing a Molecular Dynamics Calculation Unit role.

stubQM. Stub program for interface sample and testing, playing a Cycle Quantum Mechanics Calculation Unit role.

stubDI. Stub program for interface sample and testing, playing an external Domain Identifier Calculation Unit role.